MS Word's Clippy suddenly taking a level in badass might seem out of nowhere, if not for the Rule of Cool. However, it could also be considered that Clippy had always known how to fight, probably to the point where it was the only thing he was ever good at, hence how awkward and useless he is at trying to help you in the non-fighting department.
The Second Coming's instant knowledge and speed of crafting in vs. Minecraft may look like it came out of nowhere, but in the fourth installment, recall that he made a working ray gun out of Flash's tool icons, and he did it rather quickly.
In part 4, there appears to be an Esoteric Happy Ending going on when you consider the Animator still has to explain that the Facebook shenanigans weren't his fault. On the surface, it seemed doomed to be a Cassandra Truth, and it would be in our world. However, he's talking about what happened in 3 with a friend completely casually and the friend doesn't show any signs of disbelief. Combine this with the side-ad about stick figure enslavement in 3 and it's entirely possible that stick figures coming to life is a semi-regular occurrence, which would make the Animator's alibi more believable. In addition, now that he and the Second Coming are friends, the latter could have just decided to show himself and own up to the deeds.
Liking a Facebook post usually means you agree with the person in what they said. This adds a bit of Alternate Character Interpretation to the stick figure when he likes the "I give up on life" post. Perhaps he too gave up on life, especially since it happens just after his friends die.